Strain identifier

BacDive ID: 1384

Type strain: Yes

Species: Paraliobacillus ryukyuensis

Strain Designation: O15-7

Strain history: CIP <- 2003, IAM <- M. Ishikawa, Tokyo Univ. Agriculture, Tokyo, Japan

NCBI tax ID(s): 200904 (species)

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General

@ref: 5633

BacDive-ID: 1384

DSM-Number: 15140

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, motile

description: Paraliobacillus ryukyuensis O15-7 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from decomposing algae.

NCBI tax id

  • NCBI tax id: 200904
  • Matching level: species

strain history

@refhistory
5633<- K. Yamasato, Univ. Agric., Tokyo
67770IAM 15001 <-- M. Ishikawa O15-7.
122325CIP <- 2003, IAM <- M. Ishikawa, Tokyo Univ. Agriculture, Tokyo, Japan

doi: 10.13145/bacdive1384.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Paraliobacillus
  • species: Paraliobacillus ryukyuensis
  • full scientific name: Paraliobacillus ryukyuensis Ishikawa et al. 2003

@ref: 5633

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Paraliobacillus

species: Paraliobacillus ryukyuensis

full scientific name: Paraliobacillus ryukyuensis Ishikawa et al. 2003

strain designation: O15-7

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes96.022
69480100positive
122325yesrod-shaped

colony morphology

  • @ref: 122325

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5633BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
34312Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122325CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5633positivegrowth30mesophilic
34312positivegrowth30mesophilic
67770positivegrowth30mesophilic
122325positivegrowth22-37
122325nogrowth10psychrophilic
122325nogrowth45thermophilic
122325nogrowth55thermophilic

culture pH

  • @ref: 122325
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 122325
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes99.577
122325yes

halophily

@refsaltgrowthtested relationconcentration
122325NaClpositivegrowth0-4 %
122325NaClnogrowth6 %
122325NaClnogrowth8 %
122325NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol+builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose+builds acid from28066
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371amygdalin+builds acid from27613
68371methyl alpha-D-glucopyranoside+builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
122325citrate-carbon source16947
122325esculin-hydrolysis4853
122325hippurate-hydrolysis606565
122325nitrate-reduction17632
122325nitrite-reduction16301

metabolite production

  • @ref: 122325
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12232515688acetoin+
12232517234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
122325oxidase-
122325beta-galactosidase+3.2.1.23
122325alcohol dehydrogenase-1.1.1.1
122325gelatinase+/-
122325amylase+
122325caseinase+3.4.21.50
122325catalase+1.11.1.6
122325tween esterase-
122325gamma-glutamyltransferase-2.3.2.2
122325lecithinase-
122325lipase-
122325lysine decarboxylase-4.1.1.18
122325ornithine decarboxylase-4.1.1.17
122325protease-
122325urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122325--++------++---++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122325+/---+-+---+/-+++----+--++/-++/-++++--+----+++/-++----+-+/--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122325++--+--+-++----+-++---+---+++----+-------+---------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5633decomposing algaeForeshore site in Okinawa prefectureJapanJPNAsia
67770Decomposing algaOujima Islet, Okinawa Pref.JapanJPNAsia
122325Decomposing algaJapanJPNAsia1998

isolation source categories

Cat1Cat2Cat3
#Host#Algae
#Host#Plants#Decomposing plant

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
56331Risk group (German classification)
1223251Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paraliobacillus ryukyuensis gene for 16S rRNA, partial sequence, strain: NBRC 100001AB6811201490ena200904
20218Paraliobacillus ryukyuensis gene for 16S rRNAAB0878281500ena200904

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paraliobacillus ryukyuensis DSM 15140GCA_003315295scaffoldncbi200904
66792Paraliobacillus ryukyuensis strain DSM 15140200904.4wgspatric200904
66792Paraliobacillus ryukyuensis DSM 151402770939501draftimg200904

GC content

  • @ref: 67770
  • GC-content: 35.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes90.139no
flagellatedyes89.866no
gram-positiveyes87.223no
anaerobicno98.254no
aerobicyes51.888no
halophileyes93.73no
spore-formingyes89.37no
glucose-utilyes86.896no
thermophileno98.824no
glucose-fermentno61.155no

External links

@ref: 5633

culture collection no.: DSM 15140, JCM 21472, CIP 108014, IAM 15001, NBRC 100001, NRIC 0520, NBRC 10001

straininfo link

  • @ref: 71035
  • straininfo: 362271

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12501437Paraliobacillus ryukyuensis gen. nov., sp. nov., a new Gram-positive, slightly halophilic, extremely halotolerant, facultative anaerobe isolated from a decomposing marine alga.Ishikawa M, Ishizaki S, Yamamoto Y, Yamasato KJ Gen Appl Microbiol10.2323/jgam.48.2692002Bacteria, Anaerobic/classification/growth & development/*isolation & purification, Catalase/biosynthesis, Eukaryota/*microbiology, Glucose/pharmacology, Gram-Positive Bacteria/classification/growth & development/*isolation & purification, Hydrogen-Ion Concentration, RNA, Ribosomal, 16S/genetics, Sodium Chloride/pharmacology, *Water MicrobiologyEnzymology
Phylogeny19126718Paraliobacillus quinghaiensis sp. nov., isolated from salt-lake sediment in China.Chen YG, Cui XL, Zhang YQ, Li WJ, Wang YX, Xu LH, Wen ML, Peng Q, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.65735-02009Bacillaceae/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fresh Water/*microbiology, Genes, rRNA, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species SpecificityPhenotype
Phylogeny22297696Alkalilactibacillus ikkensis, gen. nov., sp. nov., a novel enzyme-producing bacterium from a cold and alkaline environment in Greenland.Schmidt M, Prieme A, Johansen A, Stougaard PExtremophiles10.1007/s00792-012-0430-72012Enzymology
Phylogeny28036251Paraliobacillus sediminis sp. nov., isolated from East China sea sediment.Cao WR, Guo LY, Du ZJ, Das A, Saren G, Jiang MY, Dunlap CA, Rooney AP, Yu XK, Li TGInt J Syst Evol Microbiol10.1099/ijsem.0.0017672017Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34232854Paraliobacillus salinarum sp. nov., isolated from saline soil in Yingkou, China.Yin YL, Li FL, Du XY, Zhang YX, Wang LInt J Syst Evol Microbiol10.1099/ijsem.0.0048772021Bacillaceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34426860Description of Lujinxingia vulgaris sp. nov., isolated from coastal sediment via prey-traps.Wang S, Mu DS, Li GY, Du ZJAntonie Van Leeuwenhoek10.1007/s10482-021-01640-52021Bacillaceae, Bacterial Typing Techniques, Bacteroidetes, China, DNA, Bacterial/genetics, Fatty Acids/analysis, *Geologic Sediments, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, *Seawater, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5633Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15140)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15140
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
34312Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5590
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71035Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362271.1StrainInfo: A central database for resolving microbial strain identifiers
122325Curators of the CIPCollection of Institut Pasteur (CIP 108014)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108014